[Insight-developers] Re: Update on GE5 Image Reading (STILL NEED SCANS!)

[Hans Johnson]

Bill,

THANKS.  Your efforts on this are greatly appreciated.  I¹ll try to test it
out later this week.

Hans
-- 
Hans J. Johnson, Ph.D.
Hans-johnson at uiowa.edu

278 GH
The University of Iowa
Iowa City, IA 52241
(319) 353 8587



From: Bill Lorensen <bill.lorensen at gmail.com>
Date: Wed, 24 Oct 2007 17:38:29 -0400
To: kent williams <norman-k-williams at uiowa.edu>
Cc: ITK <insight-developers at itk.org>, Hans Johnson <hans-johnson at uiowa.edu>,
Steve Pieper <pieper at bwh.harvard.edu>
Subject: Re: Update on GE5 Image Reading (STILL NEED SCANS!)

Kent,
 
My changes sort the files also, if necessary. Also, the origin computation
was wrong.
 
 
Bill
 
On 10/24/07, kent williams <norman-k-williams at uiowa.edu> wrote:
> Mea Maxima Culpa -- the GE file formats Image I/O stuff is the very first
> ITK code I wrote, and there is more than a little ugliness involved there
> unfortunately.  I was converting code from BRAINS2 to the ITK way.
> 
> Anyway, I have a fix that I can check in that makes images look much better.
> As near as I can figure, the sorting of slice files was backwards in some
> cases.  It was even worse than that really -- itk::GE5ImageIO was looking at
> fields in the GE5/Signa/Genesis file header that don't really mean what the
> code thought it meant.
> 
> Someone (Bill Lorensen is one suspect) added the code to generate direction
> cosines directly from the GE5 file header, so I started using that instead
> of undocumented fields in the header to recover the orientation.  That
> DirCosine code is as far as I know correct.
> 
> But, the test images were coming in swapped in one dimension or another.
> What I finally figured out is that the code that sorted the 2D files before
> moving data into a 3D buffer wasn't using the right sort order, at all. So I
> added code to set the sort order right, based on the image orientation.
> 
> I THINK I have it licked but I'm still not finding good, unambiguous test
> data.  I can tell where the top of the skull and the nose are, but bilateral
> symmetry means I can't tell when there's a L/R swap.
> 
> Fucang was kind enough to find me a few good sample files.  But does anyone
> have any GE5 files where there's some indication of which is left and right?
> Something like the 'vitaman E cap on the left temple' trick would be ideal.
> 
> Speaking of sample files:
> 
> This directory http://128.196.98.224/Public/Imaging/Event/MGH/New/ is
> supposed to be an example of an axially oriented GE5 file.  If you load it
> into Slicer3 (for example) it looks way way ugly. Not clear to me why, but
> Slicer3 displays the volume as a skewed frustrum, as though every coronal
> slice is offset in the Y direction from it's neighbors.
> 



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